An operon is a set of genes controlled by a single DNA binding protein. Multiple operons controlled by the same repressor are grouped together as a regulon. A modulon is a regulon concerned with multiple pathways or functions, in which operons may be under individual controls as well as common, pleiotropic regulatory protein.
For example: the CAP modulon contains all regulons/operons, such as the lac operon and ara regulon, that are regulated by CAP/cAMP, but each operon has other regulators as well.